Quality rootstocks are mandatory to fortify and boost up the citrus industry. Traditionally, Pakistani citrus industry is based on
two rootstocks (rough lemon and sour orange), and consequently facing many biotic and abiotic constraints. Characterization
and evaluation of new rootstocks is also essential to expand the citrus genetic resources for better utilization and to improve
future breeding programmes. In this study thirteen rootstocks were assessed based on twenty-five morphological traits
(quantitative and qualitative) whereas genetic diversity was evaluated by using forty RAPD markers. Results manifested huge
morphological diversity in Sachian Citromello, Citromello 1452, Yuma citrange and Benton rootstocks. Thirteen RAPD
markers proved reliable and effective tool and showed significant amplification, producing a total of 286 fragments with
61.53% polymorphism. Moreover, RAPD markers showed the individuality of all the studied rootstocks and highlighted the
similarities and dissimilarities among them. Findings of this study will provide basis for further investigations looking to the
improvement of citrus rootstocks. Results are also valuable for future rootstock breeding programs, particularly in release of
superior and trustworthy new rootstocks for Pakistani citrus industry. The combination of such kinds of morphological and
molecular markers is highly powerful tool in accomplishing detailed analysis of Citrus phylogeny and origin

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